I have a Blues Junior modded to hell and I love it. I run it either with a Eminence Texas Heat or through a G12H 2x12 cab and it is a real blaster of an amp.
The first fix is to reduce the V1 tube from a 12AX7 to a 5751 or a 12AT7. I know people are pretty macho on these boards about gain, but the 12AX7 at V1 floods too much gain into the pre-amp circuit making it harder. I use 3 GE 5751s for my tubes which retain a good overdrive response but allow you to use pedals without things turning to mush.
The BillM mods are easy - I have most of BillM's mods -
http://home.comcast.net/~machrone/bluesjunior.htmHis cable dress mod is easy and really takes some of the problem of some of the A note oscillation.
You could do the twin stack mod without removing the board if you have a soldering iron. The ability to dial out the middle control totally allows you much better cleans - its a real revelation on the tone of the amp. The power supply stiffening mod cures the A note resonance and also improves the bass response and can be done in less than ten minutes without taking the board out.
The other PCB mods are easy but removing the board itself is an utter bitch - it takes lots of careful patience. The bass response is improved by the tone stack mod - in fact the amp ceases to be Fender bright when you've done them all and you have a great tone.
Once you've done them all - the BJ has great grunt and great bass response - things like the presence control mod and the clean boost have to be bought from Bill and are a bit tricky.
The Hammond 1750H output transformer is directly compatible and also gives more power - but you do have to drill a hole in the PCB (a non printed part).
As to speakers - I wouldn't bother with an Alnico Blue - its too light a speaker: Fender are notorious for their wattage to be based on clean sound which means that a 15 watt speaker in a 15 watt Fender is likely to blow. The best speakers for this amp in my view and the opinion of most modders of this amp is the Eminence Texas Heat followed by a broken in G12H30 - The Texas Heat improves the bass response, the warmth and produces a break up that is sympathetic with the amp.